def create_workflow_test_script(inputfile):
myvars = get_variables()
# set up testing directory tree
wtdir = myvars['workflow_test_directory']
mast_test_dir = os.path.join(wtdir, "no_directory_yet")
while not (os.path.isdir(mast_test_dir)):
timestamp = time.strftime("%Y%m%dT%H%M%S")
mast_test_dir = os.path.join(wtdir, "output_test_%s" % timestamp)
if not (os.path.isdir(mast_test_dir)):
shutil.copytree("%s/mini_mast_tree" % wtdir, mast_test_dir)
# set up output file and submission script
shortname = inputfile.split(".")[0]
output = "%s/output_%s" % (wtdir, shortname)
submitscript = "%s/submit_%s.sh" % (wtdir, shortname)
generic_script = "%s/generic_mast_workflow.sh" % wtdir
bashcommand = "bash %s %s %s %s %s %s >> %s" % (
generic_script, mast_test_dir, myvars["workflow_examples_located"],
inputfile, myvars["workflow_activate_command"],
myvars["workflow_testing_environment"], output)
submitfile = MASTFile()
submitfile.data.append(bashcommand + "\n")
submitfile.to_file(submitscript)
return [mast_test_dir, submitscript, output]
def create_archive_files(self):
"""Save off archive files.
Returns:
creates archive_input_options.txt
creates archive_recipe_plan.txt
"""
inputsave = MASTFile()
inputsave.data = repr(self.input_options)
inputsave.to_file(
os.path.join(self.working_directory, 'archive_input_options.txt'))
recipesave = MASTFile()
recipesave.data = repr(self.recipe_plan)
recipesave.to_file(
os.path.join(self.working_directory, 'archive_recipe_plan.txt'))
#pickle_plan = os.path.join(self.working_directory, 'archive_recipe_plan.pickle')
#pm = PickleManager(pickle_plan)
#pm.save_variable(self.recipe_plan)
#pickle_options = os.path.join(self.working_directory, 'archive_input_options.pickle')
#pm = PickleManager(pickle_options)
#pm.save_variable(self.input_options)
#create the *.py input script
#ipc_obj = InputPythonCreator(input_options=self.input_options)
#ipc_filename = ipc_obj.write_script(self.working_directory, 'archive_input_options.py')
return
def test_update_children(self):
topmetad = MASTFile("files/top_metadata_single")
topmetad.data.append("origin_dir = %s/files\n" %
testdir) #give origin directory
topmetad.to_file("recipedir/metadata.txt")
#metad = MASTFile("files/metadata_single")
#metad.to_file("%s/metadata.txt" % ingdir)
rp = RecipePlan("%s/recipedir" % testdir)
rp.ingredients['ing1'] = "I"
kdict = dict()
kdict['mast_program'] = 'vasp'
kdict['mast_xc'] = 'pw91'
kdict['mast_kpoints'] = [1, 2, 3, "G"]
rp.ingred_input_options['ing1'] = dict()
rp.ingred_input_options['ing1'][
'name'] = "%s/ing1" % rp.working_directory
rp.ingred_input_options['ing1']['program_keys'] = kdict
rp.ingred_input_options['ing1'][
'structure'] = pymatgen.io.vaspio.Poscar.from_file(
"files/perfect_structure").structure
rp.update_methods['ing1'] = dict()
rp.update_methods['ing1']['ing2a'] = [['give_structure']]
rp.update_methods['ing1']['ing2b'] = [[
'give_structure_and_restart_files'
]]
rp.update_children('ing1')
self.assertTrue(os.path.isfile("recipedir/ing2a/POSCAR"))
self.assertTrue(os.path.isfile("recipedir/ing2b/POSCAR"))
#CHGCAR softlink only sent to second child
self.assertFalse(os.path.exists("recipedir/ing2a/CHGCAR"))
self.assertTrue(os.path.exists("recipedir/ing2b/CHGCAR"))
def status_change_recommended(self, iname):
"""Check if a status change is recommended for the ingredient,
as listed in the ingredient folder/change_status.txt.
Args:
iname <str>: ingredient name
Returns:
True if a status change was recommended, and
changes the status of the ingredient in self.ingredients.
False otherwise
"""
statuspath = os.path.join(self.working_directory, iname, "change_status.txt")
if not os.path.isfile(statuspath):
return False
statusfile = MASTFile(statuspath)
newdata=list()
changed=False
for sline in statusfile.data: #status:recommend:timestamp
if not "status_changed" in sline:
newstatus = sline.split(":")[0]
self.ingredients[iname]=newstatus
newline = sline + ":status_changed:" + time.asctime() + "\n"
self.logger.info("Status of %s changed to %s" % (iname, newstatus))
changed=True
newdata.append(newline)
else:
newdata.append(sline)
statusfile.data=list(newdata)
statusfile.to_file(statuspath)
return changed
def test_update_children(self):
topmetad = MASTFile("files/top_metadata_single")
topmetad.data.append("origin_dir = %s/files\n" % testdir) #give origin directory
topmetad.to_file("recipedir/metadata.txt")
#metad = MASTFile("files/metadata_single")
#metad.to_file("%s/metadata.txt" % ingdir)
rp = RecipePlan("%s/recipedir" % testdir)
rp.ingredients['ing1'] = "I"
kdict=dict()
kdict['mast_program']='vasp'
kdict['mast_xc']='pw91'
kdict['mast_kpoints']=[1,2,3,"G"]
rp.ingred_input_options['ing1']=dict()
rp.ingred_input_options['ing1']['name']="%s/ing1" % rp.working_directory
rp.ingred_input_options['ing1']['program_keys']=kdict
rp.ingred_input_options['ing1']['structure']=pymatgen.io.vaspio.Poscar.from_file("files/perfect_structure").structure
rp.update_methods['ing1']=dict()
rp.update_methods['ing1']['ing2a']=[['give_structure']]
rp.update_methods['ing1']['ing2b']=[['give_structure_and_restart_files']]
rp.update_children('ing1')
self.assertTrue(os.path.isfile("recipedir/ing2a/POSCAR"))
self.assertTrue(os.path.isfile("recipedir/ing2b/POSCAR"))
#CHGCAR softlink only sent to second child
self.assertFalse(os.path.exists("recipedir/ing2a/CHGCAR"))
self.assertTrue(os.path.exists("recipedir/ing2b/CHGCAR"))
def change_my_status(self, newstatus):
"""Change an ingredient status by writing the new status to
change_status.txt in the ingredient folder, to get picked
up by the recipe plan.
Args:
newstatus <str>: New status to which to change the ingredient.
"""
ingdir = self.keywords['name']
oneup = os.path.dirname(ingdir)
tryrecipe = os.path.basename(oneup)
statuspath = ""
if dirutil.dir_is_in_scratch(tryrecipe):
statuspath = "%s/change_status.txt" % ingdir
else:
twoup = os.path.dirname(oneup)
tryrecipe = os.path.basename(twoup)
if dirutil.dir_is_in_scratch(tryrecipe):
statuspath = "%s/change_status.txt" % oneup
else:
raise MASTError(self.__class__.__name__, "Cannot change status of ingredient %s as recipe %s or %s is not found in $MAST_SCRATCH." % (self.keywords['name'],oneup, twoup))
if os.path.isfile(statuspath):
statusfile = MASTFile(statuspath)
else:
statusfile=MASTFile()
statusfile.data.append("%s:recommend:%s" % (newstatus, time.asctime()))
statusfile.to_file(statuspath)
self.logger.info("Recommending status change to %s" % newstatus)
def create_workflow_test_script(inputfile):
myvars = get_variables()
# set up testing directory tree
wtdir=myvars['workflow_test_directory']
mast_test_dir=os.path.join(wtdir,"no_directory_yet")
while not (os.path.isdir(mast_test_dir)):
timestamp=time.strftime("%Y%m%dT%H%M%S")
mast_test_dir = os.path.join(wtdir,"output_test_%s" % timestamp)
if not (os.path.isdir(mast_test_dir)):
shutil.copytree("%s/mini_mast_tree" % wtdir, mast_test_dir)
# set up output file and submission script
shortname = inputfile.split(".")[0]
output="%s/output_%s" % (wtdir, shortname)
submitscript="%s/submit_%s.sh" % (wtdir, shortname)
generic_script="%s/generic_mast_workflow.sh" % wtdir
bashcommand="bash %s %s %s %s %s %s >> %s" % (generic_script,
mast_test_dir,
myvars["workflow_examples_located"],
inputfile,
myvars["workflow_activate_command"],
myvars["workflow_testing_environment"],
output)
submitfile=MASTFile()
submitfile.data.append(bashcommand + "\n")
submitfile.to_file(submitscript)
return [mast_test_dir, submitscript, output]
def test_write_ingredient(self):
topmetad = MASTFile("files/top_metadata_single")
topmetad.data.append("origin_dir = %s/files\n" %
testdir) #give origin directory
topmetad.to_file("recipedir/metadata.txt")
#metad = MASTFile("files/metadata_single")
#metad.to_file("%s/metadata.txt" % ingdir)
rp = RecipePlan("recipedir")
rp.ingredients['ing2b'] = "I"
kdict = dict()
kdict['mast_program'] = 'vasp'
kdict['mast_xc'] = 'pw91'
kdict['mast_kpoints'] = [1, 2, 3, "G"]
rp.ingred_input_options['ing2b'] = dict()
rp.ingred_input_options['ing2b']['name'] = "recipedir/ing2b"
rp.ingred_input_options['ing2b']['program_keys'] = kdict
rp.ingred_input_options['ing2b'][
'structure'] = pymatgen.io.vaspio.Poscar.from_file(
"files/perfect_structure").structure
rp.write_methods['ing2b'] = [['write_singlerun']]
rp.write_ingredient('ing2b')
self.assertTrue(os.path.isfile('recipedir/ing2b/INCAR'))
self.assertTrue(os.path.isfile('recipedir/ing2b/POSCAR'))
self.assertTrue(os.path.isfile('recipedir/ing2b/POTCAR'))
self.assertTrue(os.path.isfile('recipedir/ing2b/KPOINTS'))
self.assertTrue(os.path.isfile('recipedir/ing2b/submit.sh'))
def test_write_phonon_single(self):
ingdir = "writedir/single_phonon_label1"
topmetad = MASTFile("files/top_metadata_single_phonon")
topmetad.data.append("origin_dir = %s/files\n" %
testdir) #give origin directory
topmetad.to_file("writedir/metadata.txt")
metad = MASTFile("files/metadata_single_phonon")
metad.to_file("%s/metadata.txt" % ingdir)
kdict = dict()
kdict['mast_kpoints'] = [3, 3, 3, "G"]
kdict['mast_xc'] = 'pbe'
kdict['mast_program'] = 'vasp'
kdict['mast_phonon_settings'] = dict()
kdict['mast_phonon_settings']['phonon_center_site'] = "0.33 0.25 0.0"
kdict['mast_phonon_settings']['phonon_center_radius'] = "1"
kdict['mast_phonon_settings']['threshold'] = "0.075"
my_structure = pymatgen.io.vaspio.Poscar.from_file(
"files/perfect_structure").structure
mywi = ChopIngredient(name=ingdir,
program_keys=kdict,
structure=my_structure)
mywi.write_phonon_single()
self.assertTrue(mywi.checker.is_ready_to_run())
compare_phon_single = MASTFile("files/phon_single_POSCAR")
phon_singlepos = MASTFile("%s/POSCAR" % ingdir)
self.assertEqual(phon_singlepos.data, compare_phon_single.data)
def evaluate_ga_vasp_and_update(self, childname=""):
"""Evaluate the Genetic Algorithm VASP ingredient.
"""
raise NotImplementedError
childpath = os.path.join(os.path.dirname(self.keywords['name']), childname)
from mastlib.amy_ga_code import fitness_evaluation
from MAST.ingredients.checker import VaspChecker
from MAST.utility import MASTFile
dircontents = os.listdir(self.keywords['name'])
subfolders = list()
for diritem in dircontents:
fulldir = os.path.join(self.keywords['name'],diritem)
if os.path.isdir(fulldir) and diritem.isdigit():
subfolders.append(fulldir)
energylist = list()
structurelist = list()
for subfolder in subfolders:
mychecker = VaspChecker(subfolder, self.keywords['program_keys'], self.keywords['structure'])
mystructure = mychecker.get_final_structure_from_directory()
structurelist.append(mystructure)
myenergy = mychecker.get_energy_from_energy_file()
energylist.append(myenergy)
[fitoutput, fitstructure] = fitness_evaluation.evaluate(structurelist, energylist)
#If output is a structure or xyz file, could just write it directly.
fitfile = MASTFile()
fitfile.data = fitoutput
import time
timestamp = time.strftime("%Y%m%d_%H%M%S")
outputname = "my_output_%s" % timestamp
outputstrname = "my_structure_%s" % timestamp
fitfile.to_file(os.path.join(childpath, outputname))
fitstructure.write_file(os.path.join(childpath, outputstrname))
return " %s and %s written in %s" % (outputname, outputstrname, childpath)
def test_give_neb_structures_to_neb(self):
ingdir = "%s/writedir/neb_labelinit-labelfin" % testdir
recipedir = "%s/writedir" % testdir
topmetad = MASTFile("files/top_metadata_neb")
topmetad.data.append("origin_dir = %s/files\n" %
testdir) #give origin directory
topmetad.to_file("writedir/metadata.txt")
metad = MASTFile("files/metadata_neb")
metad.to_file("%s/metadata.txt" % ingdir)
kdict = dict()
kdict['mast_program'] = 'vasp_neb'
kdict['mast_neb_settings'] = dict()
kdict['mast_neb_settings']['images'] = 3
my_structure = pymatgen.io.vaspio.Poscar.from_file(
"files/perfect_structure").structure
myrelaxed = dict()
for subdir in ['00', '01', '02', '03', '04']:
os.mkdir("writedir/neb_labelinit-labelfin/%s" % subdir)
myrelaxed[subdir] = MASTFile("files/POSCAR_%s" % subdir)
myrelaxed[subdir].to_file(
"writedir/neb_labelinit-labelfin/%s/CONTCAR" % subdir)
myuci = ChopIngredient(name=ingdir,
program_keys=kdict,
structure=my_structure)
myuci.give_neb_structures_to_neb("next_ingred")
for subdir in ['01', '02', '03']:
givenstr = MASTFile(
"%s/writedir/next_ingred/parent_structure_labelinit-labelfin_%s"
% (testdir, subdir))
self.assertEqual(myrelaxed[subdir].data, givenstr.data)
def test_run_staged_ingredients(self):
topmetad = MASTFile("files/top_metadata_single")
topmetad.data.append("origin_dir = %s/files\n" % testdir) #give origin directory
topmetad.to_file("recipedir/metadata.txt")
#metad = MASTFile("files/metadata_single")
#metad.to_file("%s/metadata.txt" % ingdir)
rp = RecipePlan("recipedir")
rp.ingredients['ing1']="C"
rp.ingredients['ing2a'] = "W"
rp.ingredients['ing2b'] = "S"
rp.ingredients['ing3'] = "W"
kdict=dict()
kdict['mast_program']='vasp'
kdict['mast_xc']='pw91'
kdict['mast_kpoints']=[1,2,3,"G"]
rp.ingred_input_options['ing2b']=dict()
rp.ingred_input_options['ing2b']['name']="recipedir/ing2b"
rp.ingred_input_options['ing2b']['program_keys']=kdict
rp.ingred_input_options['ing2b']['structure']=pymatgen.io.vaspio.Poscar.from_file("files/perfect_structure").structure
rp.write_methods['ing2b']=[['write_singlerun']]
rp.write_ingredient('ing2b')
rp.ready_methods['ing2b']=[['ready_singlerun']]
rp.run_methods['ing2b']=[['run_singlerun']]
rp.complete_methods['ing2b']=[['complete_singlerun']]
rp.run_staged_ingredients()
mysubmit = MASTFile("test_control/submitlist")
self.assertEquals(mysubmit.data[0],"recipedir/ing2b\n")
self.assertEquals(rp.ingredients,{'ing1':'C','ing2a':'W','ing2b':'P','ing3':'W'})
def test_run_ingredient(self):
topmetad = MASTFile("files/top_metadata_single")
topmetad.data.append("origin_dir = %s/files\n" %
testdir) #give origin directory
topmetad.to_file("recipedir/metadata.txt")
#metad = MASTFile("files/metadata_single")
#metad.to_file("%s/metadata.txt" % ingdir)
rp = RecipePlan("recipedir")
rp.ingredients['ing2b'] = "I"
kdict = dict()
kdict['mast_program'] = 'vasp'
kdict['mast_xc'] = 'pw91'
kdict['mast_kpoints'] = [1, 2, 3, "G"]
rp.ingred_input_options['ing2b'] = dict()
rp.ingred_input_options['ing2b']['name'] = "recipedir/ing2b"
rp.ingred_input_options['ing2b']['program_keys'] = kdict
rp.ingred_input_options['ing2b'][
'structure'] = pymatgen.io.vaspio.Poscar.from_file(
"files/perfect_structure").structure
rp.write_methods['ing2b'] = [['write_singlerun']]
rp.write_ingredient('ing2b')
rp.run_methods['ing2b'] = [['run_singlerun']]
rp.run_ingredient('ing2b')
mysubmit = MASTFile("test_control/submitlist")
self.assertEquals(mysubmit.data[0], "recipedir/ing2b\n")
def test_copy_a_file_child_file_exists(self):
allowed = dict()
allowed['name'] = (str, "", "Directory name")
shutil.copy('files/another_alphatest', 'childdir/alphatest')
mybc = BaseChecker(allowed, name='files')
mybc.copy_a_file('childdir', 'third_alphatest', 'alphatest')
compare = MASTFile("files/another_alphatest")
myfile = MASTFile("childdir/alphatest")
self.assertEqual(compare.data, myfile.data)
def test_print_status(self):
rp = RecipePlan("%s/recipedir" % testdir)
rp.ingredients['ing1'] = "S"
rp.ingredients['ing2a'] = "W"
rp.ingredients['ing2b'] = "C"
rp.ingredients['ing3'] = "P"
rp.print_status()
mystatus = MASTFile("recipedir/status.txt")
status_compare = MASTFile("files/status_artificial.txt")
self.assertEqual(mystatus.data, status_compare.data)
def test_give_phonon_multiple_forces_and_displacements(self):
ingdir="%s/writedir/single_phonon_label1" % testdir
recipedir="%s/writedir" % testdir
topmetad = MASTFile("files/top_metadata_single")
topmetad.data.append("origin_dir = %s/files\n" % testdir) #give origin directory
topmetad.to_file("writedir/metadata.txt")
metad = MASTFile("files/metadata_single_phonon")
metad.to_file("%s/metadata.txt" % ingdir)
mypos = MASTFile("files/phonon_initial_POSCAR")
mypos.to_file("%s/POSCAR" % ingdir)
kdict=dict()
kdict['mast_program'] = 'vasp'
my_structure = pymatgen.io.vaspio.Poscar.from_file("files/perfect_structure").structure
myxdat=dict()
mydynmat=dict()
for subdir in ['phon_01','phon_02','phon_03']:
os.mkdir("%s/%s" % (ingdir,subdir))
myxdat[subdir] = MASTFile("files/XDATCAR_%s" % subdir)
myxdat[subdir].to_file("%s/%s/XDATCAR" % (ingdir,subdir))
mydynmat[subdir] = MASTFile("files/DYNMAT_%s" % subdir)
mydynmat[subdir].to_file("%s/%s/DYNMAT" % (ingdir, subdir))
myuci = ChopIngredient(name=ingdir,program_keys=kdict, structure=my_structure)
myuci.give_phonon_multiple_forces_and_displacements("next_ingred")
newpos = MASTFile("%s/writedir/next_ingred/POSCAR_prePHON" % testdir)
newdyn = MASTFile("%s/writedir/next_ingred/DYNMAT" % testdir)
newxdat = MASTFile("%s/writedir/next_ingred/XDATCAR" % testdir)
comparepos = MASTFile("files/phonon_initial_POSCAR")
comparedyn = MASTFile("files/DYNMAT_compare")
comparexdat = MASTFile("%s/XDATCAR" % ingdir)
self.assertEqual(newpos.data, comparepos.data)
self.assertEqual(newdyn.data, comparedyn.data)
self.assertEqual(newxdat.data, comparexdat.data)
def test_run_singlerun(self):
#raise SkipTest
ingdir = "%s/writedir/single_label1" % testdir
recipedir = "%s/writedir" % testdir
topmetad = MASTFile("files/top_metadata_single")
topmetad.data.append("origin_dir = %s/files\n" %
testdir) #give origin directory
topmetad.to_file("writedir/metadata.txt")
metad = MASTFile("files/metadata_single")
metad.to_file("%s/metadata.txt" % ingdir)
kdict = dict()
kdict['mast_program'] = 'vasp'
kdict['mast_kpoints'] = [2, 2, 2, "M"]
kdict['mast_xc'] = 'pw91'
my_structure = Poscar.from_file("files/perfect_structure").structure
mywr = ChopIngredient(name=ingdir,
program_keys=kdict,
structure=my_structure)
mywr.write_singlerun()
myri = ChopIngredient(name=ingdir,
program_keys=kdict,
structure=my_structure)
myri.run_singlerun()
self.assertTrue(myri.checker.is_ready_to_run())
mysubmit = MASTFile("%s/submitlist" % self.test_control)
self.assertEquals(mysubmit.data[0], "%s\n" % ingdir)
def test_inputpythoncreator(self):
raise SkipTest
myip = InputParser(inputfile='mast.inp')
myoptions=myip.parse()
myipc = InputPythonCreator(input_options=myoptions)
mylines=myipc.print_input_options()
myfile = MASTFile()
myfile.data = mylines
myfile.to_file("./input_python_created")
#print mylines
self.assertTrue(filecmp.cmp("input_python_created","test_input_python_created"))
def test_start(self):
#rfile=os.path.join(testdir,'personalized')
wdir=os.path.join(testdir,'workdir')
struc=None
iopt=MAST.parsers.inputparser.InputParser(inputfile='input.inp').parse()
rfile = iopt.get_item('personal_recipe', 'personal_recipe_list')
myrs=RecipeSetup(recipeFile=rfile, workingDirectory=wdir, inputOptions=iopt, structure=struc)
myrs.start()
compare_metadata=MASTFile('compare_metadata.txt')
myrs_metadata=MASTFile(os.path.join(wdir,'metadata.txt'))
self.assertEqual(myrs_metadata.data, compare_metadata.data)
dirlist=MAST.utility.dirutil.walkdirs(wdir)
print dirlist
compare_dirlist=list()
compare_dirlist.append('defect_1nn_q=p0_opt1')
compare_dirlist.append('defect_1nn_q=p0_opt2')
compare_dirlist.append('defect_1nn_q=p0_stat')
compare_dirlist.append('defect_purefin_q=p0_opt1')
compare_dirlist.append('defect_purefin_q=p0_opt2')
compare_dirlist.append('defect_purefin_q=p0_stat')
compare_dirlist.append('defect_pureinit_q=p0_opt1')
compare_dirlist.append('defect_pureinit_q=p0_opt2')
compare_dirlist.append('defect_pureinit_q=p0_stat')
compare_dirlist.append('defect_solute_q=p0_opt1')
compare_dirlist.append('defect_solute_q=p0_opt2')
compare_dirlist.append('defect_solute_q=p0_stat')
compare_dirlist.append('diffcoeff_utility')
compare_dirlist.append('inducedefect_1nn')
compare_dirlist.append('inducedefect_purefin')
compare_dirlist.append('inducedefect_pureinit')
compare_dirlist.append('inducedefect_solute')
compare_dirlist.append('neb_1nn-solute_q=p0_opt1')
compare_dirlist.append('neb_1nn-solute_q=p0_opt2')
compare_dirlist.append('neb_1nn-solute_q=p0_stat')
compare_dirlist.append('neb_pureinit-purefin_q=p0_opt1')
compare_dirlist.append('neb_pureinit-purefin_q=p0_opt2')
compare_dirlist.append('neb_pureinit-purefin_q=p0_stat')
compare_dirlist.append('perfect_opt1')
compare_dirlist.append('perfect_opt2')
compare_dirlist.append('perfect_stat')
compare_dirlist.append('phonon_1nn-solute_q=p0_movingsolute')
compare_dirlist.append('phonon_1nn_q=p0_solute')
compare_dirlist.append('phonon_pureinit-purefin_q=p0_movingsolvent')
compare_dirlist.append('phonon_pureinit_q=p0_solvent')
compare_dirlist_withpath=list()
for diritem in compare_dirlist:
compare_dirlist_withpath.append(os.path.join(wdir,diritem))
mdiff=self.maxDiff
self.maxDiff=None
self.assertItemsEqual(dirlist,compare_dirlist_withpath)
self.maxDiff=mdiff
def test_get_my_phonon_params(self):
ingdir = "writedir/single_phonon_label1"
topmetad = MASTFile("files/top_metadata_single_phonon")
topmetad.data.append("origin_dir = %s/files\n" %
testdir) #give origin directory
topmetad.to_file("writedir/metadata.txt")
metad = MASTFile("files/metadata_single_phonon")
metad.to_file("%s/metadata.txt" % ingdir)
kdict = dict()
kdict['mast_kpoints'] = [3, 3, 3, "G"]
kdict['mast_xc'] = 'pbe'
kdict['mast_program'] = 'vasp'
kdict['mast_phonon_settings'] = dict()
kdict['mast_phonon_settings']['phonon_center_site'] = "0.33 0.25 0.0"
kdict['mast_phonon_settings']['phonon_center_radius'] = "1"
kdict['mast_phonon_settings']['threshold'] = "0.075"
my_structure = pymatgen.io.vaspio.Poscar.from_file(
"files/perfect_structure").structure
mywi = ChopIngredient(name=ingdir,
program_keys=kdict,
structure=my_structure)
[mysite, myrad, mythresh] = mywi.get_my_phonon_params()
self.assertEqual(mysite, "0.33 0.25 0.0")
self.assertEqual(myrad, "1")
self.assertEqual(mythresh, "0.075")
def test_ready_neb_subfolders(self):
ingdir = "%s/writedir/single_label1" % testdir
recipedir = "%s/writedir" % testdir
topmetad = MASTFile("files/top_metadata_single")
topmetad.data.append("origin_dir = %s/files\n" %
testdir) #give origin directory
topmetad.to_file("writedir/metadata.txt")
metad = MASTFile("files/metadata_single")
metad.to_file("%s/metadata.txt" % ingdir)
kdict = dict()
kdict['mast_program'] = 'vasp'
kdict['mast_kpoints'] = [2, 2, 2, "M"]
kdict['mast_xc'] = 'pw91'
kdict['mast_neb_settings'] = dict()
kdict['mast_neb_settings']['images'] = 3
my_structure = pymatgen.io.vaspio.Poscar.from_file(
"files/perfect_structure").structure
mywr = ChopIngredient(name=ingdir,
program_keys=kdict,
structure=my_structure)
for subdir in ['00', '01', '02', '03', '04']:
subname = "%s/%s" % (ingdir, subdir)
os.mkdir(subname)
mywr.keywords['name'] = subname
mywr.checker.keywords['name'] = subname
if not subdir in ['00', '04']:
mywr.write_singlerun()
mywr.write_submit_script()
myrdi = ChopIngredient(name=ingdir,
program_keys=kdict,
structure=my_structure)
self.assertTrue(myrdi.ready_neb_subfolders())
os.remove("%s/01/POSCAR" % ingdir)
self.assertFalse(myrdi.ready_neb_subfolders())
def test_ready_singlerun(self):
ingdir = "%s/writedir/single_label1" % testdir
recipedir = "%s/writedir" % testdir
topmetad = MASTFile("files/top_metadata_single")
topmetad.data.append("origin_dir = %s/files\n" %
testdir) #give origin directory
topmetad.to_file("writedir/metadata.txt")
metad = MASTFile("files/metadata_single")
metad.to_file("%s/metadata.txt" % ingdir)
kdict = dict()
kdict['mast_program'] = 'vasp'
kdict['mast_kpoints'] = [2, 2, 2, "M"]
kdict['mast_xc'] = 'pw91'
my_structure = pymatgen.io.vaspio.Poscar.from_file(
"files/perfect_structure").structure
mywr = ChopIngredient(name=ingdir,
program_keys=kdict,
structure=my_structure)
mywr.write_singlerun()
myrdi = ChopIngredient(name=ingdir,
program_keys=kdict,
structure=my_structure)
self.assertTrue(myrdi.ready_singlerun())
os.remove("%s/POSCAR" % ingdir)
self.assertFalse(myrdi.ready_singlerun())
def create_archive_files(self):
"""Save off archive files.
Returns:
creates archive_input_options.txt
creates archive_recipe_plan.txt
"""
inputsave = MASTFile()
inputsave.data = repr(self.input_options)
inputsave.to_file(os.path.join(self.working_directory, 'archive_input_options.txt'))
recipesave = MASTFile()
recipesave.data = repr(self.recipe_plan)
recipesave.to_file(os.path.join(self.working_directory, 'archive_recipe_plan.txt'))
#pickle_plan = os.path.join(self.working_directory, 'archive_recipe_plan.pickle')
#pm = PickleManager(pickle_plan)
#pm.save_variable(self.recipe_plan)
#pickle_options = os.path.join(self.working_directory, 'archive_input_options.pickle')
#pm = PickleManager(pickle_options)
#pm.save_variable(self.input_options)
#create the *.py input script
#ipc_obj = InputPythonCreator(input_options=self.input_options)
#ipc_filename = ipc_obj.write_script(self.working_directory, 'archive_input_options.py')
return
def test_get_statuses_from_file(self):
rp = RecipePlan("recipedir")
mystatus = MASTFile("files/status_random.txt")
self.assertRaises(MASTError, rp.get_statuses_from_file)
mystatus.to_file("recipedir/status.txt")
rp.ingredients['ing1']="I"
rp.ingredients['ing2a']="I"
rp.ingredients['ing2b']="I"
self.assertRaises(MASTError,rp.get_statuses_from_file)
rp.ingredients['ing3']="I"
rp.get_statuses_from_file()
statusdict=dict()
statusdict={'ing1':'alpha','ing2a':'beta','ing2b':'gamma','ing3':'delta'}
self.assertEquals(rp.ingredients, statusdict)
def test_parse_phonon_section(self):
raise SkipTest
#Phonon section in input file is now obsolete!
myip = InputParser(inputfile="neb_with_phonons.inp")
minput = MASTFile("%s/phonon_lines.txt" % testdir)
cleanlines = list()
for line in minput.data:
cleanlines.append(line.strip())
myoptions = InputOptions()
myip.parse_phonon_section('phonon', cleanlines, myoptions)
print myoptions
mdict = dict()
mdict['perfect'] = dict()
mdict['perfect']['phonon_center_site'] = '0.5 0.5 0'
mdict['perfect']['phonon_center_radius'] = '1'
mdict['vac1'] = dict()
mdict['vac1']['phonon_center_site'] = '0.5 0.5 0'
mdict['vac1']['phonon_center_radius'] = '1'
mdict['vac2'] = dict()
mdict['vac2']['phonon_center_site'] = '0.0 0.0 0'
mdict['vac2']['phonon_center_radius'] = '1'
mdict['vac1-vac2'] = dict()
mdict['vac1-vac2']['phonon_center_site'] = '0.25 0.25 0'
mdict['vac1-vac2']['phonon_center_radius'] = '1'
self.assertEqual(myoptions.options['phonon']['phonon'], mdict)
def read_input_file(self, inputtxt=""):
"""Read the input file.
Args:
inputtxt <str>: Input file name (shortname)
Returns:
Sets self.dirs with perfect and defected directories
Sets self.bandgap_lda_or_gga
Sets self.bandgap_hse_or_expt
"""
ifpath = os.path.join(self.ingdir, inputtxt)
ifile = MASTFile(ifpath)
for dline in ifile.data:
dline = dline.strip()
if dline[0] == "#":
continue
if len(dline) == 0:
continue
dsplit = dline.split("=", 1)
dkey = dsplit[0]
dval = dsplit[1]
if dkey[0:4] == "dfe_":
mylabel = dkey[4:]
myperfect = dval.split()[0]
mydefected = dval.split()[1]
self.dirs[mylabel] = dict()
self.dirs[mylabel]['perfect'] = myperfect
self.dirs[mylabel]['defected'] = mydefected
elif dkey == "bandgap_lda_or_gga":
self.bandgap_lda_or_gga = float(dval)
elif dkey == "bandgap_hse_or_expt":
self.bandgap_hse_or_expt = float(dval)
else:
pass
return
def test_parse_structure_section_noposfile(self):
myip = InputParser(inputfile="neb_with_phonons.inp")
minput = MASTFile("%s/structure_noposfile_lines.txt" % testdir)
cleanlines = list()
for line in minput.data:
cleanlines.append(line.strip())
myoptions = InputOptions()
myip.parse_structure_section('structure', cleanlines, myoptions)
#print myoptions
self.assertEqual(myoptions.options['structure']['atom_list'],
['Al', 'Mg', 'Al', 'Fe'])
self.assertEqual(myoptions.options['structure']['coord_type'],
'fractional')
self.assertTrue(
np.array_equal(myoptions.options['structure']['lattice'],
np.array([[3.5, 1, 2], [3, 3.5, 4], [5, 6, 3.5]])))
self.assertTrue(
np.array_equal(
myoptions.options['structure']['coordinates'],
np.array([[0, 0, 0], [0.5, 0.5, 0], [0, 0.5, 0.5],
[0.5, 0, 0.5]])))
self.assertItemsEqual(myoptions.options['structure']['element_map'],
dict({
'X1': 'Al',
'X2': 'Mg',
'X3': 'Fe'
}))
def main(ingname=""):
"""Get the last lattice from an ingredient.
Args:
ingname <str>: Ingredient name, full path
Returns:
<string>: "Last lattice (Angstroms);scale, a, b, c", ex:
"Last lattice (Angstroms); scale 1, 4.01 0.2 0, 0 4.01 0,
0.1 0.1 4.01"
"""
trymeta = "%s/metadata.txt" % ingname
frontstr = "Last lattice (Angstroms);"
if os.path.isfile(trymeta):
mymeta = Metadata(metafile=trymeta)
myprogram = mymeta.read_data("program")
else:
myprogram = "None"
if myprogram in ['vasp', 'vasp_neb']:
if os.path.isdir("%s/01" % ingname):
tryfile = "%s/01/CONTCAR" % ingname
else:
tryfile = "%s/CONTCAR" % ingname
cfile = MASTFile(tryfile)
if len(cfile.data) == 0:
return "%s N/A" % frontstr
scale = cfile.data[1].strip()
avec = cfile.data[2].strip()
bvec = cfile.data[3].strip()
cvec = cfile.data[4].strip()
return "%s scale %s, %s, %s, %s" % (frontstr, scale, avec, bvec, cvec)
else:
return "%s N/A" % frontstr
def test_simple_optimization(self):
[mystatus, my_test_dir
] = workflow_setup.generic_submit("simple_optimization.inp")
if mystatus == "Unfinished":
self.assertTrue(False)
return
elif mystatus == "Completed":
recipedir = workflow_setup.get_finished_recipe_dir(my_test_dir)
myfile = MASTFile(os.path.join(recipedir, "SUMMARY.txt"))
okays = 0
for myline in myfile.data:
if "defect_int1_stat" in myline:
myenergy = myline.split()[-1]
self.assertEquals(myenergy, "-13.953")
okays = okays + 1
if "defect_vac1_stat" in myline:
myenergy = myline.split()[-1]
self.assertEquals(myenergy, "-10.623")
okays = okays + 1
if "defect_sub1_stat" in myline:
myenergy = myline.split()[-1]
self.assertEquals(myenergy, "-20.145")
okays = okays + 1
self.assertEquals(okays, 3)
return
else:
self.assertTrue(False)
return
def print_table(self,scsize):
if not self.e_defects:
self._calculate_defect_formation_energies(scsize)
myfile = MASTFile()
for conditions, defects in self.e_defects.items():
myfile.data.append('\n\nDefect formation energies for %s conditions.\n' % conditions.upper())
myfile.data.append('%-20s | %10s\n' % ('Defect', 'DFE'))
myfile.data.append('---------------------------------\n')
for defect, energies in defects.items():
for energy in energies:
myfile.data.append('%-14s(q=%2i) | %8.4f\n' % (defect, energy[0], energy[1]))
myfile.data.append(str()) # Add a blank line here
myfile.data.append('---------------------------------\n')
myfile.to_file(os.path.join(os.getcwd(),"dfe.txt"))
for line in myfile.data:
print line.strip()
def test_vasp_kpoints_setup_from_metafile(self):
kdict = dict()
mymeta = MASTFile("childdir/metadata.txt")
mymeta.data.append("kpoints = 3x1x7 G 0.5 0.2 .1\n")
mymeta.to_file("childdir/metadata.txt")
mymeta2 = MASTFile("childdir/metadata.txt")
print mymeta2.data
myvc = VaspChecker(name="childdir", program_keys=kdict)
mykpt = myvc._vasp_kpoints_setup()
kpt_compare = pymatgen.io.vaspio.Kpoints.from_file("files/KPOINTS_317G")
self.assertEqual(kpt_compare.kpts[0][0], mykpt.kpts[0][0])
self.assertEqual(kpt_compare.kpts[0][1], mykpt.kpts[0][1])
self.assertEqual(kpt_compare.kpts[0][2], mykpt.kpts[0][2])
self.assertEqual(kpt_compare.num_kpts, mykpt.num_kpts)
self.assertEqual(kpt_compare.style, mykpt.style)
# self.assertEqual(kpt_compare.kpts_shift, mykpt.kpts_shift)
self.assertEqual((0.5, 0.2, 0.1), mykpt.kpts_shift)
def test_dfe_tool(self):
import subprocess
os.chdir("archive/GaAs_defects_AsGa_recipe_defects_20131125T220427/dfe_ingredient")
mydfetest=subprocess.Popen(["mast_defect_formation_energy dfe_input.txt"],shell=True)
mydfetest.wait()
os.chdir(testdir)
compare_walk = dirutil.walkfiles("compare_results")
compare_walk.remove("compare_results/__init__.py")
compare_walk.remove("compare_results/__init__.pyc")
res_walk = dirutil.walkfiles("archive/GaAs_defects_AsGa_recipe_defects_20131125T220427/dfe_ingredient/dfe_results")
compare_walk.sort()
res_walk.sort()
self.assertEqual(len(compare_walk), len(res_walk))
for idx in range(0,len(compare_walk)):
compfile = MASTFile(compare_walk[idx])
myfile = MASTFile(res_walk[idx])
self.assertEqual(compfile.data, myfile.data)
def main(mydir="", fname="", startat=0, childdir=""):
"""This method makes POSCAR-containing subfolders from a
list of structures,
in childdir if a child directory is given, or in
mydir otherwise.
File fname must reside in directory mydir.
Args:
mydir <str>: Ingredient directory
fname <str>: File containing list of structures
startat <str, will be converted to int>:
0 (default) - start subfolders at 00
1 - start subfolders at 01
childdir <str>: Child directory (optional)
If xyz files, fname is required to be of the form:
"xyz"
<float a> <float b> <float c for box size>
fileone.xyz
filetwo.xyz
...
If POSCAR or other structure files, fname may simply
start with file names:
POSCAR_01
POSCAR_02
"""
logger = logging.getLogger(mydir)
logger = loggerutils.add_handler_for_recipe(mydir, logger)
if childdir == "":
childdir = mydir
fpath = os.path.join(mydir, fname)
if not os.path.isfile(fpath):
logger.error("No file found at %s" % fpath)
return "File not found. No effect."
str_list_file = MASTFile(fpath)
if str_list_file.data[0].strip().lower() == "xyz":
namelist = list(str_list_file.data[2:])
structure_list = get_xyz_structures(mydir, str_list_file.data[1],
namelist)
else:
namelist = list(str_list_file.data)
structure_list = get_structures(mydir, namelist)
if not (len(structure_list) == len(namelist)):
logger.error("Not all structures in file %s found." % fname)
return "Not all structures found. No effect."
strct = int(startat)
for one_structure in structure_list:
subname = str(strct).zfill(2)
subpath = os.path.join(childdir, subname)
if not os.path.isdir(subpath):
os.mkdir(subpath)
one_poscar = pymatgen.io.vaspio.Poscar(one_structure)
pospath = os.path.join(subpath, "POSCAR")
if os.path.isfile(pospath):
logger.error("POSCAR file already exists at %s" % subpath)
else:
one_poscar.write_file(os.path.join(subpath, "POSCAR"))
strct = strct + 1
return "Wrote all POSCAR files to subdirectories in %s" % childdir
def test_vasp_kpoints_setup_from_metafile(self):
kdict = dict()
mymeta = MASTFile("childdir/metadata.txt")
mymeta.data.append("kpoints = 3x1x7 G 0.5 0.2 .1\n")
mymeta.to_file("childdir/metadata.txt")
mymeta2 = MASTFile("childdir/metadata.txt")
print mymeta2.data
myvc = VaspChecker(name="childdir", program_keys=kdict)
mykpt = myvc._vasp_kpoints_setup()
kpt_compare = pymatgen.io.vaspio.Kpoints.from_file(
"files/KPOINTS_317G")
self.assertEqual(kpt_compare.kpts[0][0], mykpt.kpts[0][0])
self.assertEqual(kpt_compare.kpts[0][1], mykpt.kpts[0][1])
self.assertEqual(kpt_compare.kpts[0][2], mykpt.kpts[0][2])
self.assertEqual(kpt_compare.num_kpts, mykpt.num_kpts)
self.assertEqual(kpt_compare.style, mykpt.style)
#self.assertEqual(kpt_compare.kpts_shift, mykpt.kpts_shift)
self.assertEqual((0.5, 0.2, 0.1), mykpt.kpts_shift)
def check(self):
errfilepath = queue_commands.get_job_error_file(self.ingpath)
self.logger.info("Checking file at %s" % errfilepath)
if errfilepath == None:
return False
errfile = MASTFile(errfilepath)
for errline in errfile.data:
if 'insufficient virtual memory' in errline.lower():
return True
def test_complete_ingredient(self):
topmetad = MASTFile("files/top_metadata_single")
topmetad.data.append("origin_dir = %s/files\n" % testdir) #give origin directory
topmetad.to_file("recipedir/metadata.txt")
#metad = MASTFile("files/metadata_single")
#metad.to_file("%s/metadata.txt" % ingdir)
rp = RecipePlan("recipedir")
rp.ingredients['ing1'] = "I"
kdict=dict()
kdict['mast_program']='vasp'
kdict['mast_xc']='pw91'
kdict['mast_kpoints']=[1,2,3,"G"]
rp.ingred_input_options['ing1']=dict()
rp.ingred_input_options['ing1']['name']="%s/recipedir/ing1" % testdir
rp.ingred_input_options['ing1']['program_keys']=kdict
rp.ingred_input_options['ing1']['structure']=pymatgen.io.vaspio.Poscar.from_file("files/perfect_structure").structure
rp.complete_methods['ing1']=[['complete_singlerun']]
self.assertTrue(rp.complete_ingredient('ing1'))
def check_recipe_dir(self, fulldir, verbose, single_ingred_mode):
"""Check a recipe directory.
Args:
fulldir <str>: full path of recipe directory
verbose <int>: verbosity
single_ingred_mode <str>: 0 for checking all ingredients
ingredient name for checking a single ingredient
"""
shortdir = os.path.basename(fulldir) #only the recipe directory name
if not os.path.exists(fulldir):
raise MASTError(self.__class__.__name__,
"No recipe directory at %s" % fulldir)
if os.path.exists(os.path.join(fulldir, "MAST_SKIP")):
self.logger.warning(
"Skipping recipe %s due to the presence of a MAST_SKIP file in the recipe directory."
% shortdir)
return
if os.path.exists(os.path.join(fulldir, "MAST_ERROR")):
self.logger.error(
"ATTENTION!: Skipping recipe %s due to the presence of a MAST_ERROR file in the recipe directory."
% shortdir)
return
self.logger.info("--------------------------------")
self.logger.info("Processing recipe %s" % shortdir)
self.logger.info("--------------------------------")
my_recipe_plan_object = self.set_up_recipe_plan(fulldir, verbose)
os.chdir(fulldir) #need to change directories in order to submit jobs?
try:
my_recipe_plan_object.check_recipe_status(verbose,
single_ingred_mode)
except Exception:
import sys, traceback
#ex_type, ex, trbck = sys.exc_info()
errortext = traceback.format_exc()
#del trbck
errorfile = open(os.path.join(fulldir, "MAST_ERROR"), "ab")
errorfile.write("ERROR LOGGED %s\n" % time.asctime())
errorfile.write("%s\n" % errortext)
errorfile.close()
self.logger.warning(
"ERROR in recipe %s. Check MAST_ERROR file in the %s directory."
% (shortdir, fulldir))
#raise MASTError(self.__class__.__name__,"Error in recipe %s as follows: %s %s %s" % (shortdir, ex_type, ex, errortext))
os.chdir(self.scratch)
if my_recipe_plan_object.status == "C":
shutil.move(fulldir, self._ARCHIVE)
summarypath = "%s/%s/SUMMARY.txt" % (self._ARCHIVE, shortdir)
if os.path.isfile(summarypath):
self.logger.info("Recipe %s completed." % shortdir)
self.logger.info("SUMMARY.txt below:")
summarytext = MASTFile(summarypath)
for myline in summarytext.data:
self.logger.info(myline.strip())
self.logger.info("-----------------------------")
self.logger.info("Recipe %s processed." % shortdir)
self.logger.info("-----------------------------")
def get_variables():
verify_checks()
myvars = dict()
checkfile = MASTFile(checkname)
for myline in checkfile.data:
if myline[0:9] == "workflow_":
mykey = myline.split("=")[0].strip()
myval = myline.split("=")[1].strip()
myvars[mykey] = myval
return myvars
def test_get_statuses_from_file(self):
rp = RecipePlan("recipedir")
mystatus = MASTFile("files/status_random.txt")
self.assertRaises(MASTError, rp.get_statuses_from_file)
mystatus.to_file("recipedir/status.txt")
rp.ingredients['ing1'] = "I"
rp.ingredients['ing2a'] = "I"
rp.ingredients['ing2b'] = "I"
self.assertRaises(MASTError, rp.get_statuses_from_file)
rp.ingredients['ing3'] = "I"
rp.get_statuses_from_file()
statusdict = dict()
statusdict = {
'ing1': 'alpha',
'ing2a': 'beta',
'ing2b': 'gamma',
'ing3': 'delta'
}
self.assertEquals(rp.ingredients, statusdict)
def check(self):
errfilepath = queue_commands.get_job_error_file(self.ingpath)
if errfilepath == None:
return False
errfile = MASTFile(errfilepath)
for errline in errfile.data:
if 'walltime' in errline.lower():
return True
elif 'time limit' in errline.lower():
return True
def create_archive_files(self):
"""Save off archive files.
Returns:
creates archive_input_options.txt
creates archive_recipe_plan.txt
"""
inputsave = MASTFile()
inputsave.data = repr(self.input_options)
inputsave.to_file(
os.path.join(self.recdir,
'archive_input_options_%s.txt' % self.timestamp))
recipesave = MASTFile()
recipesave.data = repr(self.recipe_plan)
recipesave.to_file(
os.path.join(self.recdir,
'archive_recipe_plan_%s.txt' % self.timestamp))
return
def main():
recipe_name, script_head_dir = parse_arguments()
mast_scratch = dirutil.get_mast_scratch_path()
mymon = MASTMon()
my_recipe_plan = mymon.set_up_recipe_plan(os.path.join(mast_scratch, recipe_name), 1)
my_dag_contents=list()
for iname in my_recipe_plan.ingredients: #all JOB lines need to be at top
my_dag_contents.append("JOB %s submit.sh DIR %s\n" % (iname, iname))
for iname in my_recipe_plan.ingredients:
my_dag_contents.append("SCRIPT PRE %s %s/mast_do_setup.sh %s %s\n" % (iname, script_head_dir, recipe_name, iname))
my_dag_contents.append("SCRIPT POST %s %s/mast_check_is_complete.sh %s %s\n" % (iname, script_head_dir, recipe_name, iname))
my_dag_contents.append("RETRY %s 5\n" % iname)
ptc = list(my_recipe_plan.parents_to_check[iname])
for pname in ptc:
my_dag_contents.append("PARENT %s CHILD %s\n" % (pname, iname))
my_dag_file = MASTFile()
my_dag_file.data = my_dag_contents
my_dag_file.to_file(os.path.join(mast_scratch, recipe_name, "recipe.dag"))
#print_to_file(recipe_name, ing_name, "MAIN: is complete: %s" % is_complete)
return 0
def test_give_structure(self):
ingdir="%s/writedir/single_label1" % testdir
recipedir="%s/writedir" % testdir
topmetad = MASTFile("files/top_metadata_single")
topmetad.data.append("origin_dir = %s/files\n" % testdir) #give origin directory
topmetad.to_file("writedir/metadata.txt")
metad = MASTFile("files/metadata_single")
metad.to_file("%s/metadata.txt" % ingdir)
kdict=dict()
kdict['mast_program'] = 'vasp'
my_structure = pymatgen.io.vaspio.Poscar.from_file("files/perfect_structure").structure
myrelaxed = MASTFile("files/relaxed_structure")
myrelaxed.to_file("%s/CONTCAR" % ingdir)
myuci = ChopIngredient(name=ingdir,program_keys=kdict, structure=my_structure)
myuci.give_structure("next_ingred")
givenstr = MASTFile("%s/writedir/next_ingred/POSCAR" % testdir)
self.assertEqual(myrelaxed.data, givenstr.data)
def test_give_saddle_structure(self):
ingdir="%s/writedir/neb_labelinit-labelfin" % testdir
recipedir="%s/writedir" % testdir
topmetad = MASTFile("files/top_metadata_neb")
topmetad.data.append("origin_dir = %s/files\n" % testdir) #give origin directory
topmetad.to_file("writedir/metadata.txt")
metad = MASTFile("files/metadata_neb")
metad.to_file("%s/metadata.txt" % ingdir)
kdict=dict()
kdict['mast_program'] = 'vasp_neb'
kdict['images'] = 3
my_structure = pymatgen.io.vaspio.Poscar.from_file("files/perfect_structure").structure
myrelaxed=dict()
myosz=dict()
mywav=dict()
mychg=dict()
for subdir in ['00','01','02','03','04']:
os.mkdir("writedir/neb_labelinit-labelfin/%s" % subdir)
myrelaxed[subdir] = MASTFile("files/POSCAR_%s" % subdir)
myrelaxed[subdir].to_file("writedir/neb_labelinit-labelfin/%s/CONTCAR" % subdir)
myosz[subdir] = MASTFile("files/OSZICAR_%s" % subdir)
myosz[subdir].to_file("writedir/neb_labelinit-labelfin/%s/OSZICAR" % subdir)
mychg[subdir] = MASTFile("files/CHGCAR")
mychg[subdir].to_file("writedir/neb_labelinit-labelfin/%s/CHGCAR" % subdir)
mywav[subdir] = MASTFile("files/WAVECAR")
mywav[subdir].to_file("writedir/neb_labelinit-labelfin/%s/WAVECAR" % subdir)
myuci = ChopIngredient(name=ingdir,program_keys=kdict, structure=my_structure)
myuci.give_saddle_structure("next_ingred") #should be OSZ3
saddle = MASTFile("%s/writedir/next_ingred/POSCAR" % testdir)
self.assertEqual(myrelaxed['03'].data, saddle.data)
saddledir = myuci.get_saddle_dir()
self.assertEqual(saddledir, "03")
def test_check_if_ready_to_proceed_are_complete(self):
metad = MASTFile("files/metadata_single")
metad.to_file("recipedir/ing1/metadata.txt")
metad = MASTFile("files/metadata_single")
metad.to_file("recipedir/ing2a/metadata.txt")
rp = RecipePlan("recipedir")
rp.ingredients['ing1'] = "P"
rp.ingredients['ing2a'] = "I"
rp.ingredients['ing2b'] = "I"
rp.ingredients['ing3'] = "I"
kdict=dict()
kdict['mast_program']='vasp'
kdict['mast_xc']='pw91'
kdict['mast_kpoints']=[1,2,3,"G"]
my_struc = pymatgen.io.vaspio.Poscar.from_file("files/perfect_structure").structure
rp.ingred_input_options['ing1']=dict()
rp.ingred_input_options['ing1']['name']="%s/recipedir/ing1" % testdir
rp.ingred_input_options['ing1']['program_keys']=kdict
rp.ingred_input_options['ing1']['structure']=my_struc
rp.complete_methods['ing1']=[['complete_singlerun']]
rp.update_methods['ing1']=dict()
rp.update_methods['ing1']['ing2a']=[['give_structure']]
rp.update_methods['ing1']['ing2b']=[['give_structure']]
rp.ingred_input_options['ing2a']=dict()
rp.ingred_input_options['ing2a']['name']="%s/recipedir/ing2a" % testdir
rp.ingred_input_options['ing2a']['program_keys']=kdict
rp.ingred_input_options['ing2a']['structure']=my_struc
rp.complete_methods['ing2a']=[['complete_singlerun']]
rp.ready_methods['ing2a']=[['ready_structure']]
rp.check_if_ready_to_proceed_are_complete()
self.assertTrue(rp.ready_ingredient('ing2a'))
self.assertEquals
self.assertEquals(rp.ingredients,{'ing1':'C','ing2a':'I','ing2b':'I','ing3':'I'})
def test_run_subfolders(self):
#raise SkipTest
ingdir="%s/writedir/single_label1" % testdir
recipedir="%s/writedir" % testdir
topmetad = MASTFile("files/top_metadata_single")
topmetad.data.append("origin_dir = %s/files\n" % testdir) #give origin directory
topmetad.to_file("writedir/metadata.txt")
metad = MASTFile("files/metadata_single")
metad.to_file("%s/metadata.txt" % ingdir)
kdict=dict()
kdict['mast_program'] = 'vasp'
kdict['mast_kpoints'] = [2,2,2,"M"]
kdict['mast_xc'] = 'pw91'
my_structure = Poscar.from_file("files/perfect_structure").structure
for subfolder in ['sub1','sub2','sub3','sub4']:
subname = "%s/%s" % (ingdir, subfolder)
os.mkdir(subname)
shutil.copy("files/metadata_single","%s/metadata.txt" % subname)
mywr = ChopIngredient(name=subname, program_keys = kdict, structure=my_structure)
mywr.write_singlerun()
myri = ChopIngredient(name=ingdir,program_keys=kdict, structure=my_structure)
myri.run_subfolders()
self.assertFalse(myri.checker.is_ready_to_run())
for subfolder in ['sub1','sub2','sub3','sub4']:
subname = "%s/%s" % (ingdir, subfolder)
myri.checker.keywords['name'] = subname
self.assertTrue(myri.checker.is_ready_to_run())
mysubmit = MASTFile("%s/submitlist" % self.test_control)
self.assertEquals(mysubmit.data[0], "%s/sub1\n" % ingdir)
self.assertEquals(mysubmit.data[1], "%s/sub2\n" % ingdir)
self.assertEquals(mysubmit.data[2], "%s/sub3\n" % ingdir)
self.assertEquals(mysubmit.data[3], "%s/sub4\n" % ingdir)
def test_ready_neb_subfolders(self):
ingdir="%s/writedir/single_label1" % testdir
recipedir="%s/writedir" % testdir
topmetad = MASTFile("files/top_metadata_single")
topmetad.data.append("origin_dir = %s/files\n" % testdir) #give origin directory
topmetad.to_file("writedir/metadata.txt")
metad = MASTFile("files/metadata_single")
metad.to_file("%s/metadata.txt" % ingdir)
kdict=dict()
kdict['mast_program'] = 'vasp'
kdict['mast_kpoints'] = [2,2,2,"M"]
kdict['mast_xc'] = 'pw91'
kdict['mast_neb_settings']=dict()
kdict['mast_neb_settings']['images'] = 3
my_structure = pymatgen.io.vaspio.Poscar.from_file("files/perfect_structure").structure
mywr = ChopIngredient(name=ingdir, program_keys = kdict, structure=my_structure)
for subdir in ['00','01','02','03','04']:
subname = "%s/%s" % (ingdir, subdir)
os.mkdir(subname)
mywr.keywords['name'] = subname
mywr.checker.keywords['name'] = subname
if not subdir in ['00','04']:
mywr.write_singlerun()
mywr.write_submit_script()
myrdi = ChopIngredient(name=ingdir,program_keys=kdict, structure=my_structure)
self.assertTrue(myrdi.ready_neb_subfolders())
os.remove("%s/01/POSCAR" % ingdir)
self.assertFalse(myrdi.ready_neb_subfolders())
def create_archive_files(self):
"""Save off archive files.
Returns:
creates archive_input_options.txt
creates archive_recipe_plan.txt
"""
inputsave = MASTFile()
inputsave.data = repr(self.input_options)
inputsave.to_file(os.path.join(self.recdir, 'archive_input_options_%s.txt' % self.timestamp))
recipesave = MASTFile()
recipesave.data = repr(self.recipe_plan)
recipesave.to_file(os.path.join(self.recdir, 'archive_recipe_plan_%s.txt' % self.timestamp))
return
def test_write_ingredient(self):
topmetad = MASTFile("files/top_metadata_single")
topmetad.data.append("origin_dir = %s/files\n" % testdir) #give origin directory
topmetad.to_file("recipedir/metadata.txt")
#metad = MASTFile("files/metadata_single")
#metad.to_file("%s/metadata.txt" % ingdir)
rp = RecipePlan("recipedir")
rp.ingredients['ing2b'] = "I"
kdict=dict()
kdict['mast_program']='vasp'
kdict['mast_xc']='pw91'
kdict['mast_kpoints']=[1,2,3,"G"]
rp.ingred_input_options['ing2b']=dict()
rp.ingred_input_options['ing2b']['name']="recipedir/ing2b"
rp.ingred_input_options['ing2b']['program_keys']=kdict
rp.ingred_input_options['ing2b']['structure']=pymatgen.io.vaspio.Poscar.from_file("files/perfect_structure").structure
rp.write_methods['ing2b']=[['write_singlerun']]
rp.write_ingredient('ing2b')
self.assertTrue(os.path.isfile('recipedir/ing2b/INCAR'))
self.assertTrue(os.path.isfile('recipedir/ing2b/POSCAR'))
self.assertTrue(os.path.isfile('recipedir/ing2b/POTCAR'))
self.assertTrue(os.path.isfile('recipedir/ing2b/KPOINTS'))
self.assertTrue(os.path.isfile('recipedir/ing2b/submit.sh'))
def test_parse(self):
#ipfile='small_workflow_with_scaling.inp'
ipfile='phonon_with_neb.inp'
workdir = os.path.join(testdir,'workdir')
shutil.copy(os.path.join(testdir,ipfile),workdir)
input_file = os.path.join(workdir,ipfile)
parser_obj = InputParser(inputfile=input_file)
input_options = parser_obj.parse()
recipe_file_contents = input_options.get_item('recipe','recipe_file')
myrtp = RecipeTemplateParser(inputOptions=input_options,
working_directory=workdir,
templateFile=recipe_file_contents,
personalRecipe=input_file)
parsed_lines = myrtp.parse()
output_parsed = MASTFile()
output_parsed.data = list(parsed_lines)
output_parsed.to_file('workdir/personal_recipe_test_output.txt')
self.assertEquals(len(myrtp.chunks),5)
#mypr = MASTFile(pr)
#for line in mypr.data:
# print line.rstrip()
compare_pr = MASTFile(os.path.join(testdir,'compare','personal_recipe_test_output.txt'))
self.assertEquals(parsed_lines, compare_pr.data)
def test_run_strain(self):
#raise SkipTest
ingdir="%s/writedir/single_label1" % testdir
recipedir="%s/writedir" % testdir
topmetad = MASTFile("files/top_metadata_single")
topmetad.data.append("origin_dir = %s/files\n" % testdir) #give origin directory
topmetad.to_file("writedir/metadata.txt")
metad = MASTFile("files/metadata_single")
metad.to_file("%s/metadata.txt" % ingdir)
kdict=dict()
kdict['mast_program'] = 'vasp'
kdict['mast_strain']=" 0.98 0.92 1.03 \n"
my_structure = Poscar.from_file("files/POSCAR_perfect").structure
myunstrained = MASTFile("files/POSCAR_unstrained")
myunstrained.to_file("%s/POSCAR" % ingdir)
myri = ChopIngredient(name=ingdir,program_keys=kdict, structure=my_structure)
myri.run_strain()
my_strained = Poscar.from_file("%s/CONTCAR" % ingdir).structure
strained_compare = Poscar.from_file("files/POSCAR_strained").structure
self.assertEquals(my_strained, strained_compare)
self.assertFalse(os.path.isfile("%s/submitlist" % self.test_control))
def test_run_scale(self):
#raise SkipTest
ingdir="%s/writedir/single_label1" % testdir
recipedir="%s/writedir" % testdir
topmetad = MASTFile("files/top_metadata_single")
topmetad.data.append("origin_dir = %s/files\n" % testdir) #give origin directory
topmetad.to_file("writedir/metadata.txt")
metad = MASTFile("files/metadata_single")
metad.data.append("defect_label = label1\n")
metad.data.append("scaling_size = [2,2,2]\n")
metad.to_file("%s/metadata.txt" % ingdir)
kdict=dict()
kdict['mast_program'] = 'vasp'
my_structure = Poscar.from_file("files/POSCAR_perfect").structure
myperf = MASTFile("files/POSCAR_perfect")
myperf.to_file("%s/POSCAR" % ingdir)
myri = ChopIngredient(name=ingdir,program_keys=kdict, structure=my_structure)
myri.run_scale()
my_scaled = Poscar.from_file("%s/CONTCAR" % ingdir).structure.get_sorted_structure()
scaled_compare = Poscar.from_file("files/POSCAR_scaled").structure.get_sorted_structure()
self.assertEquals(my_scaled, scaled_compare)
def test__fullpath_childname(self):
ingdir="%s/writedir/single_label1" % testdir
topmetad = MASTFile("files/top_metadata_single")
topmetad.data.append("origin_dir = %s/files\n" % testdir) #give origin directory
topmetad.to_file("writedir/metadata.txt")
metad = MASTFile("files/metadata_single")
metad.to_file("%s/metadata.txt" % ingdir)
kdict=dict()
kdict['mast_program'] = 'vasp'
my_structure = pymatgen.io.vaspio.Poscar.from_file("files/perfect_structure").structure
myuci = ChopIngredient(name=ingdir,program_keys=kdict,structure=my_structure)
fullpath = myuci._fullpath_childname("next_ingred")
self.assertEqual(fullpath, "%s/writedir/next_ingred" % testdir)
def test_set_up_program_input(self):
mystrs=list()
pos=dict()
for posstr in ['00','01','02','03','04']:
pos[posstr] = pymatgen.io.vaspio.Poscar.from_file("structures/POSCAR_%s" % posstr)
mystrs.append(pos[posstr].structure)
kdict=dict()
kdict['mast_kpoints']=[3,3,3,"G"]
kdict['mast_xc']="pw91"
kdict['mast_neb_settings']=dict()
kdict['mast_neb_settings']['images']=3
kdict['mast_neb_settings']['image_structures'] = mystrs
myvcneb=VaspNEBChecker(name="childdir",program_keys=kdict)
myvcneb.set_up_program_input()
submitscript = MASTFile()
submitscript.data="Submission script placeholder."
submitscript.to_file("childdir/submit.sh")
ozholder = MASTFile()
ozholder.data="OSZICAR placeholder."
submitscript.to_file("childdir/00/OSZICAR")
submitscript.to_file("childdir/04/OSZICAR")
self.assertTrue(myvcneb.is_ready_to_run())
def test_write_singlerun(self):
ingdir="writedir/single_label1"
topmetad = MASTFile("files/top_metadata_single")
topmetad.data.append("origin_dir = %s/files\n" % testdir) #give origin directory
topmetad.to_file("writedir/metadata.txt")
metad = MASTFile("files/metadata_single")
metad.to_file("%s/metadata.txt" % ingdir)
kdict=dict()
kdict['mast_kpoints']=[3,3,3,"G"]
kdict['mast_xc']='pbe'
kdict['mast_program']='vasp'
my_structure=pymatgen.io.vaspio.Poscar.from_file("files/perfect_structure").structure
mywi = ChopIngredient(name=ingdir,program_keys=kdict,structure=my_structure)
mywi.write_singlerun()
self.assertTrue(mywi.checker.is_ready_to_run())
def test_ready_structure(self):
ingdir="%s/writedir/single_label1" % testdir
recipedir="%s/writedir" % testdir
topmetad = MASTFile("files/top_metadata_single")
topmetad.data.append("origin_dir = %s/files\n" % testdir) #give origin directory
topmetad.to_file("writedir/metadata.txt")
metad = MASTFile("files/metadata_single")
metad.to_file("%s/metadata.txt" % ingdir)
kdict=dict()
kdict['mast_program'] = 'vasp'
kdict['mast_kpoints'] = [2,2,2,"M"]
kdict['mast_xc'] = 'pw91'
my_pos = pymatgen.io.vaspio.Poscar.from_file("files/perfect_structure")
my_pos.write_file("writedir/single_label1/POSCAR")
myrdi = ChopIngredient(name=ingdir,program_keys=kdict, structure=my_pos.structure)
self.assertTrue(myrdi.ready_structure())
os.remove("%s/POSCAR" % ingdir)
self.assertFalse(myrdi.ready_structure())
def test_write_singlerun_automesh(self):
ingdir="writedir/single_label1"
topmetad = MASTFile("files/top_metadata_single")
topmetad.data.append("origin_dir = %s/files\n" % testdir) #give origin directory
topmetad.to_file("writedir/metadata.txt")
metad = MASTFile("files/metadata_single")
metad.to_file("%s/metadata.txt" % ingdir)
kdict=dict()
kdict['mast_kpoints']=[3,3,3,"G"]
kdict['mast_xc']='pbe'
kdict['mast_program']='vasp'
kdict['mast_kpoint_density']='1000'
mypos=pymatgen.io.vaspio.Poscar.from_file("files/perfect_structure")
mypos.write_file("writedir/single_label1/POSCAR")
mywi = ChopIngredient(name=ingdir,program_keys=kdict,structure=mypos.structure)
mywi.write_singlerun_automesh()
mykpts = pymatgen.io.vaspio.Kpoints.from_file("writedir/single_label1/KPOINTS")
self.assertEqual(mykpts.to_dict['kpoints'][0],[8,8,8])
#print mykpts
self.assertTrue(mywi.checker.is_ready_to_run())
def test_run_singlerun(self):
#raise SkipTest
ingdir="%s/writedir/single_label1" % testdir
recipedir="%s/writedir" % testdir
topmetad = MASTFile("files/top_metadata_single")
topmetad.data.append("origin_dir = %s/files\n" % testdir) #give origin directory
topmetad.to_file("writedir/metadata.txt")
metad = MASTFile("files/metadata_single")
metad.to_file("%s/metadata.txt" % ingdir)
kdict=dict()
kdict['mast_program'] = 'vasp'
kdict['mast_kpoints'] = [2,2,2,"M"]
kdict['mast_xc'] = 'pw91'
my_structure = Poscar.from_file("files/perfect_structure").structure
mywr = ChopIngredient(name=ingdir, program_keys = kdict, structure=my_structure)
mywr.write_singlerun()
myri = ChopIngredient(name=ingdir,program_keys=kdict, structure=my_structure)
myri.run_singlerun()
self.assertTrue(myri.checker.is_ready_to_run())
mysubmit = MASTFile("%s/submitlist" % self.test_control)
self.assertEquals(mysubmit.data[0], "%s\n" % ingdir)